Miniaturized fluorescence analysis system

ABSTRACT

According to embodiments of the present invention, a fluorescence analysis system includes a light emitting diode (LED) array to excite a fluorophor sample for analysis. The system includes an LED array driver that pulses the LEDs in the array with currents in excess of maximum rated current at low duty cycles to reduce LED degradation over time. An LED selection optimization process and software select the LEDs to be included in the array from among various colors and currents to be applied. The LED selection optimization process and software take filters and attenuation into consideration.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.60/606,000, filed Aug. 31, 2004.

GOVERNMENT LICENSE RIGHTS

The U.S. Government has a paid-up license in this invention and theright in limited circumstances to require the patent owner to licenseothers on reasonable terms as provided for by the terms of Grant No. NIH1-P50-HG002360-01.

BACKGROUND

1. Field

Embodiments of the present invention relate to fluorescence analysissystems and in particular to light emitting diode (LED)-basedfluorescence analysis systems.

2. Discussion of Related Art

Fluorescence is the emission of light by molecules which have absorbedlight. The fluorescing characteristics of such molecules (calledfluorophors) are useful in detecting and tagging various microbiologicalevents. The emission signal is shifted to higher wavelengths(Stokes-Shift) in relation to the excitation signal because the energyof the fluorescing light emitted is less than the light absorbed by thefluorophor.

Fluorometers exploit the fluorescing property of fluorophor molecules inthe analysis of biological samples. The simulation and optimization of aLED-based fluorometer should ideally maximize the efficiency with whichlight is converted to signal (emission) and minimize bleed-throughexcitation light to the output signal path. In other words, the overlapbetween excitation light source and emission spectra should be minimizedso that once the excitation light is optically filtered from the outputsignal, maximum emission signal remains for measurement.

Conventional fluorescence analysis systems use a laser or a high powerwhite light source (e.g. Xenon lamp) to excite fluorophors in the sampleunder analysis. LEDs (light emitting diodes) are of interest to replaceconventional light sources to increase the portability (reduce power,size, and weight) of the analysis system and to improve the flexibilityof excitation spectra available to the user with reduced opticsoverhead. Several approaches have been used in LED-based fluorescenceanalysis systems. LEDs are an attractive alternative to conventionalwhite light sources used in fluorescence analysis because of reducedpower of operation, fewer imaging artifacts, and increased flexibilityin spectral control without the need for high overhead optics.

General purpose, commercially available portable systems, such as theTurner Biosystems [1][2] instruments have used single LEDs to excitefluorescing samples; these systems rely on the user to select the LED tomatch the fluorophor or vice versa. Many results in the literature relyon single or small arrays of LEDs, where excitation bands are chosenclose to the excitation spectra of the fluorophor and the resultingemission spectrum is optically filtered to minimize interference fromthe excitation signal. Still other approaches excite a sample usingdifferent LEDs at different times and subsequent signal processing toimprove the extraction of the emission signal from the combined outputsignal. Finally, a variety of waveguides have been constructed tominimize the transfer of excitation light along the output emission pathat the expense of reduced sample volume.

The use of LEDs, however, is often limited by three primary factors: (a)the broadband output of an LED often interferes with the measurement ofemission signal; (b) the power (intensity) of light generated by an LED(mWatts) is often small compared to white light source (Watts)counterparts; and (c) the excitation peaks of the LED are often not wellmatched to the absorption efficiency of the fluorophor under analysis.The use of LEDs, for this reason, has been largely limited to highconcentration applications where emitted fluorescence is sufficientlyhigh (and noise sufficiently low) that LED limitations do not restricteffective measurements of the sample under analysis. The spectralflexibility, modularity, low-cost, and low power consumption of LEDs,however, continue to make them attractive options for fluorescenceanalysis, however.

In many approaches using LEDs, the choice of LED (or LEDs) is usuallynot optimized prior to the collection of data by the fluorescenceanalysis system. Instead, the optics and signal processing are assignedthe task of separating excitation components from the emission signal inthe output path. In addition, many LED-based fluorescence analysissystems used in commercial and research efforts are general-purpose.This means that they are suited to a relatively wide selection offluorophors and the biological applications to which they are applied.

SUMMARY OF EMBODIMENTS OF THE INVENTION

Embodiments of the present invention are directed to automated andmodular optimization of fluorescence analysis system that may maximizesignal extraction (SNR) from an excited fluorophor. In one embodiment,the system includes an array of light emitting diodes (LEDs) that emitexcitation light. The excitation light may have a first color and/orwavelength (blue, blue-green, green, purple, or other suitablecolor/wavelength. The color and/or wavelength of the excitation light ofone LED may be different than the color and/ or wavelength of anotherexcitation light of one LED.

The system also includes control electronics that apply drive currentsto the LEDs. The drive currents cause the LEDs to emit the excitationlight. The drive current to one LED may be different than the drivecurrent to another LED. For some embodiments, the drive current isgreater than nominal drive current, greater than rated maximum currentfor the LED, and in may range between twenty and two hundred milliamps.The control electronics may include an emitter follower circuit and/orsource follower circuit to drive the LEDs.

The control electronics also may pulse the drive current to the LEDswith signals having low duty cycles. For example, in one embodiment, thecontrol electronics may pulse the drive current to the LEDs with signalshaving duty cycles between one percent and twelve percent. In otherembodiments, the control electronics may pulse the drive current to theLEDs with signals having duty cycles at or greater than twelve percent.

The system also includes optics to couple excitation light from the LEDsto a holder for the fluorophor. In one embodiment, an optical fiberbundle may be coupled to each individual LED so that each LED has itsown optical fiber bundle associated with it. The optical fiber bundlesmay be bundled together so that the excitation light from the LEDs maybe aggregated into a single light beam that has a substantially uniformintensity profile and/or a substantially uniform wavelengthdistribution. The bundle of bundles couples the single light beam to thefluorophor holder. In one embodiment, the optical fiber bundles arebundled together in a random manner.

For some embodiments, the system may include a beam splitter to splitoff a small portion of the single light beam and to direct the smallportion to circuitry to measure the intensity of the small portion ofthe single light beam as a function of the color and/or wavelength. Thecircuitry may adjust drive current to one or more LEDs in response tothe measured intensity of the small portion of the single light beam.The circuitry may be a spectrophotometer.

For other embodiments, one or more PIN diode may be coupled to one ormore LEDs, respectively, to detect the excitation light emitted from theLED. There may be circuitry to adjust one or more drive currents inresponse to the detected excitation light.

When the excitation light impinges on a fluorophor placed in thefluorophor holder, the fluorophor may emit light that in response to theexcitation light. The emitted light may have a color and/or wavelengththat is different than the color and/or wavelength of the excitationlight. In one embodiment, the fluorophor holder may be a cuvette.

The system also includes a photodetector to detect light emitted fromthe fluorophor. The photodetector may a photomultiplier tube, anavalanche photodiode, photodiode, phototransistor, and/or acharge-coupled device (CCD).

The system also includes optical fiber to couple the light emitted fromthe fluorophor to the photodetector.

For some embodiments, the system may be used to select a configurationfor the LED array. The system may determine at least two possiblepermutations of LEDs for the LED array and for each permutationdetermine a total excitation light that is to be emitted from the LEDarray, determine an amount of excitation light that is to reach thefluorophor based on the total excitation light emitted from the LEDarray, determine an amount of light that is to be transmitted throughthe fluorophor based on the amount of excitation light that is to reachthe fluorophor, based on an amount of attenuation in an emission path toa photodetector from the fluorophor in the fluorescence analysis system,and based on filtering of the light that is to be transmitted throughthe fluorophor, determine an amount of light that is to be emitted bythe fluorophor based on the amount of excitation light that is to reachthe fluorophor and based on the amount of light that is to betransmitted through the fluorophor, determine an amount of light that isto reach the photodetector based on the amount of light that is to beemitted by the fluorophor, and determine a leakage penalty for thefluorescence analysis system based on the amount of light that is to betransmitted through the fluorophor and based on the amount of light thatis to reach the photodetector. The system then compares the leakagepenalties for each permutation of LEDs in the LED array and ranks thepermutations of LEDs in the LED array based on the comparison of theirrespective leakage penalties.

In one embodiment, the system may receive from a user informationassociated with a type of LEDs to be selected from a database,information associated with a number of LEDs to be placed in the LEDarray, information associated with the fluorophor of interest,information associated with at least one undesirable fluorophor,information associated with a minimum concentration detection capabilityfor the fluorophor of interest, and/ or information associated with atime frame within which to perform fluorescence analysis on thefluorophor of interest.

The system may, for each permutation of LEDs in the LED array, determineoptical power and/or spectral shape of an aggregate output of the LEDarray, receive information associated with spectral characteristics ofthe photodetector, calculate output current and/or output voltage of thephotodetector based on the information associated with the spectralcharacteristics of the photodetector, determine a drive current for eachLED in the LED array based on the leakage penalty, determine a dutycycle for the drive current based on the leakage penalty, and/ordetermine a duty cycle in the range of one percent to twelve percent forthe drive current based on the leakage penalty.

For some embodiments, optimizing software may be used to perform theabove-described method. In these embodiments, the software may be amachine-readable medium having data to cause a machine to select aconfiguration for the LED array.

As will be described below, the optimization software takes into accounta variety of factors of practical fluorescence analysis includingoptics, photodetector properties, attenuation in the sample itself, andleakage of the excitation signal to the output signal path. While mostfluorometer systems use a single light source such as a Xenon or Mercurylamp, in embodiments of the present invention the optimization softwarerelies on a combination of several LEDs in an array driven at variousnominal and overdrive currents. Overdriving the LEDs enables spectralshifts from nominal peak excitation wavelengths that increase theflexibility and intensity of spectra identified by optimizationsoftware. Given a fluorophor, environmental conditions, and optical pathconstraints, the optimization software may generate the best possiblecombination of LEDs to excite the sample and maximize the emissionsignal collected in the output path.

BRIEF DESCRIPTION OF THE DRAWINGS

In the drawings, like reference numbers generally indicate identical,functionally similar, and/or structurally equivalent elements. Thedrawing in which an element first appears is indicated by the leftmostdigit(s) in the reference number, in which:

FIG. 1 is a high-level block diagram illustrating a miniaturizedfluorescence analysis system according to an embodiment of the presentinvention;

FIG. 2 is a schematic diagram illustrating the LED driver depicted inFIG. 1 according to an embodiment of the present invention;

FIG. 3 is graphical representation illustrating experimentalmeasurements of various commercially available LEDs across time anddrive current to characterize their effective lifetime according to anembodiment of the present invention;

FIG. 4 is graphical representation illustrating experimentaldemonstration of increased lifetime of the reduced duty cycle accordingto an embodiment of the present invention;

FIG. 5 is a graphical representation illustrating an example of theeffectiveness of LED as compared to Xenon excitation according to anembodiment of the present invention;

FIGS. 6A and 6B illustrate a flowchart of operation of the systemdepicted in FIG. 1 according to an embodiment of the present invention;

FIG. 7, including 7(a), 7(b), and 7(c) is a graphical representationillustrating results generated by the process depicted in FIG. 6 forevaluating GFPuv according to an embodiment of the present invention;

FIG. 8 is a graphical representation of an emission spectrum accordingto an embodiment of the present invention;

FIG. 9 is a graphical representation of the results of LED arrayoptimization according to an embodiment of the present invention;

FIG. 10 is a graphical representation of the results of Rhodamineanalysis according to an embodiment of the present invention; and

FIG. 11 is a graphical representation of an intensity comparisonaccording to an embodiment of the present invention.

DETAILED DESCRIPTION OF THE ILLUSTRATED EMBODIMENTS

FIG. 1 is a high-level block diagram illustrating a miniaturizedfluorescence analysis system 100 according to an embodiment of thepresent invention, in which an LED array 102 is coupled to fiber opticcoupling 104. The fiber optic coupling 104 is optionally coupled to abeam splitter 106, which is part of a feed back loop. The example fiberoptic coupling 104 may be coupled to a sample 108 (e.g., fluorophor)without the feed back loop. The sample 108 is coupled to fiber opticcoupling 110, which is optionally coupled to one or more opticaldispersion devices 112. The fiber optic coupling 110 may be coupled to aphotodiode array 114 without the optical dispersion devices 112. Thephotodetector 114 (shown as a photodiode array) is coupled to a signalprocessing module 116. A monitor light source module 118 is coupled inthe feed back loop between the beam splitter 106 and the LED array 102.The illustrated module 118 includes an LED driver 120.

LEDs are traditionally less stable than their white light sourcecounterparts. In the system 100, the real-time feedback loop monitorsthe LED array 102 output and adjusts the LED array 102 drive currentsand output powers to maintain a stable signal into the fluorophor sample108. The output light passes from the LED array 102 through therandomizing fiber optic coupling 104, and into the beam splitter 106,where most of the light travels to the sample 108 (for exciting thefluorophor or other luminescing sample). A small percentage of the lightmay be fed back to a spectrophotometer in the monitor light sourcemodule 118 where it is analyzed for power and spectral properties, forexample. The spectrophotometer sends power and spectral information to amicrocontroller in the monitor light source module 118, which is thenused to adjust the LED array 102 output properties through the LEDdriver 120.

For some embodiments, the LED array 102 is a highly flexible, modularLED array having several LEDs of different types (e.g., purple, blue,blue-green, and green) operating under several different possible drivecurrents (e.g., 5 and 20 mA are nominal operating conditions and 50,100, and 150 mA are overdrive currents that not only increase theintensity of LED output but also produce fine shifts (in wavelength) ofthe spectral properties of the LED). In one embodiment, using type anddrive current as variables, the 5-element LED array can produce amaximum of 3.2 million possible aggregate spectra.

The LED driver 120 is designed to be a dynamic, feedback driven lightsource suitable for use in fluorescence analysis systems. It is designedas a solution to common drawbacks of conventional fluorescence lightsources (large cost, power, and size) and resolves issues associatedwith using LEDs as light sources for fluorescence analysis. (lowintensity, stability, and lifetime, poor spectral control). An obstacleto using LEDs as a light source for fluorescence analysis is the smalllight intensity produced as compared to a conventional light source(Xenon lamp). The LED driver 120 solves this problem by overdriving theLEDs in the LED array 102 with very high currents, up to and beyond tentimes the rated maximum current for the LED (20 mA DC), for example.Normal operation at these currents using DC may destroy the LED, but theLED driver 120 has solved this problem by pulsing the LEDs in the LEDarray 102 at these high currents for very short periods of time, in therange of 1-12% duty cycle, for example. Light intensity out of an LED isproportional to the input current, therefore each pulse of the LED mayproduce ten times the normal light intensity produced undermanufacturer's operation specifications. By pulsing the LEDs in thisway, lifetime degradation due to high currents may be reduced.

An additional side-effect of pulsing an LED at a high current with a lowduty cycle is a shift in the spectral output of the LED. As mentionedabove, one of the key problems encountered when using LEDs as a lightsource for fluorescence analysis is poor spectral control of the LEDlight output. Limited output spectra are available because LEDs areavailable only in discrete fixed wavelengths, as well as a few broadbandLEDs. Creating a broadband light source from LEDs is difficult becauseof the extreme difference between types of LEDs. Some colors have higherintensities than others, “white light” LEDs are predominantly blue, andthere can be both spectral and intensity differences between two LEDs ofthe same color and type.

These inconsistencies are solved with the LED driver 120, which adjustsintensity variations using driving current. In this manner, the spectralshift side-effect mentioned above, which is usually regarded as aninhibitor to using LEDs as light sources, is exploited to adjust thespectral output of the LEDs to match the light source needs of theapplication. By driving an array of LEDs, aggregated into a single lightsource, the LED driver 120 creates a tunable light source.

In one embodiment, the LED driver 120 may be a printed circuit board(PCB) having four high current driver circuits as shown in FIG. 2, whichis a schematic diagram of the LED driver 120 according to an embodimentof the present invention. The illustrated LED driver 120 may be capableof controlling a pair of LEDs at user adjustable duty cycles between onepercent and twelve percent and at current levels between ten milliampsand two hundred milliamps. In the LED driver 120, an emitter-follower(or source follower if using CMOS technology) supplies high current tothe driving transistor Q1. A crystal oscillator (not shown) and a seriesof counters (not shown) may supply the low duty cycle driving signal tothe LED drivers 120.

Various commercially available LEDs (blue, blue-green, purple, green)have been experimentally measured across time and drive current tocharacterize their effective lifetime. An example of thecharacterization results is shown in FIG. 3. The higher the drivecurrent, the shorter the lifetime of the LED. However, lifetimedegradation can be circumvented, for fluorescence analysis applications,by reducing the duty cycle of the LED, so that they are activated longenough to excite fluorescence, but not so long as to prematurely degradethe useful lifetime of the LED.

Experimental demonstration of increased lifetime of the reduced dutycycle approach is shown in FIG. 4 for DC operation (100% duty cycle) andlow (1%) duty cycle operation. Lifetime of the blue LED shown in theseresults improves by an average of 30% using the LED driver 120.

Using high drive currents, it is possible to achieve the power levels ofconventional light sources in practical biological analysis experiments.An example of the effectiveness of LED as compared to Xenon excitationis shown in FIG. 5. This experiment captures the fluorescence of AM1bacteria tagged with UV-GFP fluorophor. An array of 7 purple LEDsoperating at 50 mA currents are used to excite the UV-GFP taggedbacteria at comparable levels to the Xenon light source in a standardShimadzu RF3401 fluorometer. Standard growth studies are typicallyperformed over a 24 hour period with data collection occurring every 3hours. These experiment lengths cannot be accommodated with LEDs at highcurrents, using DC operation, but fall well within the limits of LEDsoperating at the reduced duty cycles controlled by the LED driver moduledescribed herein. These types of electronic interface and controlmodules are essential to the effective use of LEDs and LED arrays inlow-level fluorescence analysis.

The fiber optic coupling 104 includes an optical fiber bundle coupled toeach individual LED so that each LED. The optical fiber bundles arebundled together in a random manner to aggregate the excitation lightinto a single light beam. Without the random fiber optic coupling 104the output of the LED array 102 might be a series of discrete spots thatmay excite the sample 108 in an unpredictable and unstable manner.

The sample 108 may be held in a standard, commercially available cuvetteholder, but may be coupled within the system 100 via the fiber opticcoupling 104 and the fiber optic coupling 110 rather than traditionaloptical components. The fiber optic couplings 104 and 110 may be anysuitable single mode or multimode optical fibers. The fiber opticcouplings 104 and 110 also reduce or eliminate the need for periodic orunpredictable realignment of optics.

The photodetector 114, although shown as photodiodes, may be anyconventional photomultiplier tubes, avalanche photodiodes, low powerphotodiodes, phototransistors, charge-coupled devices that arecompatible with portable, small footprint systems. Alternativephotodetection schemes may be enabled by the reduced optical losses inthe system 100 incurred by the use of fiber optic couplings 104 and 110rather than discrete optics an the absence of slits required for whitelight sources, which also decrease optical throughput.

The LED configuration may be optimized using a design simulation programthat accounts for LED output characteristics, optical filtering andlosses, photodetector properties, sample characteristics, sampleattenuation and other factors in seeking the “best” LED configuration interms of overlap between the emission and excitation spectra, totalemission intensity (SNR), or both.

FIG. 6 is a flowchart of a process 600 illustrating operation of thesystem 100 according to an embodiment of the present invention. Theprocess 600 may be implemented using hardware, software, or acombination thereof. In implementations using software, the software maybe stored on a machine-accessible medium. In a block 602 the process 600begins and control passes to a block 604.

In a block 604, the process 600 determines at least two possiblepermutations of LEDs for the LED array 102.

In a block 606, for each permutation of LEDs in the LED array, theprocess 600 determines a total excitation light I_(IN) (λi) that is tobe emitted from the permutation of LEDs to be placed in the LED array102.

In a block 608, the process 600 determines an amount of excitation lightthat is to reach the fluorophor sample 108 based on the total excitationlight emitted from the permutation of LEDs. At a particular wavelength,λi, the light that reaches the sample 108 may be expressed as I_(S)(λi):I _(S)(λ_(i))=I _(IN)(λ_(i))×A _(L) ×F _(L)(λ_(i))   (1)

where I_(IN)(λi) is the total excitation light (Watts) impinging on thesample at wavelength λi, that is attenuated by the optical loss in theexcitation path A_(L) and by F_(L)(λi), the transmissivity of filter inthe excitation path.

In a block 610, the process 600 determines an amount of light that is tobe transmitted through the fluorophor sample 108 based on the amount ofexcitation light that is to reach the fluorophor sample 108, the amountof attenuation in the emission path to the photodetector array 114 fromthe fluorophor sample 108, and based on filtering of the light that isto be transmitted through the fluorophor sample 108. The light that istransmitted through the sample, rather than absorbed by the fluorophorcan be expressed, according to Beer's Law, in terms of the extinctioncoefficient ε(λi) to obtain I_(L) _(—) _(max)(λi):I _(L) _(—) _(max)(λ_(i))=I _(S)(λ_(i))×(10^(−ε(λ) ^(i) ^()cL))   (2)

where ε(λi) is the extinction coefficient (liters/cm*mole) at wavelengthλi and is given by the excitation spectrum for the fluorophor sample108, c is the concentration of fluorophor sample 108 in the sample(moles per liter); and L is the fluorophor sample 108 path length (cm).

The transmitted light may then be attenuated by optical losses (A_(E))and filtered (F_(E)(λi)) in the emission path to obtain I_(L)(λi):I _(L)(λ_(i))=I _(L) _(—) _(max)(λ_(i))×A _(S) ×A _(E) ×F _(E)(λ_(i))  (3)

The factor A_(S) accounts for scattering and other losses between thesample and the output optical path. The light that is not transmittedthrough the fluorophor sample 108 is absorbed.

In a block 612, the process 600 determines an amount of light that is tobe emitted by the fluorophor sample 108 based on the amount ofexcitation light that is to reach the fluorophor sample 108 and theamount of light that is to be transmitted through the fluorophor sample108. Some of this absorbed light is then emitted as fluorescence I_(E):I _(E)=(I _(S) −I _(L) _(—) _(max))×Q   (4)

where the factor Q represent fluorescence efficiency (quantum yield),and is a function of such variables as pH, temperature, and heavy metalion concentration; I_(S) and I_(L)max represent the total light reachingthe sample 108 and transmitted light, respectively, integrated acrossall wavelengths λi. The total emitted light I_(E) is redistributedacross wavelength λi according to the emission spectrum of thefluorophor sample 108 (available from the manufacturer).

In a block 614, the process 600 determines an amount of light that is toreach the photodetector array 114 based on the amount of light that isto be emitted by the fluorophor sample 108. The fluorescence signal thatreaches the photodetector array 114 at the end of the optical path isthen given by I_(E)′:I _(E)′(λ_(i))=I _(E)(λ_(i))×A _(E) ×F _(E)(λ_(i))   (5)

In a block 616, the process 600 determines a leakage penalty for thefluorescence analysis system 100 based on the amount of light that is tobe transmitted through the fluorophor sample 108 and based on the amountof light that is to reach the photodetector array 114. In order tooptimize fluorescence emission, a performance metric P is defined asfollows: $\begin{matrix}{{P\left( \lambda_{i} \right)} = \frac{I_{L}\left( \lambda_{i} \right)}{{I_{L}\left( \lambda_{i} \right)} + {I_{E}^{\prime}\left( \lambda_{i} \right)}}} & (6)\end{matrix}$

This dimensionless parameter is a measure of how much leakage from theexcitation process affects the emission signal and is analogous to thereciprocal of SNR (signal to noise ratio) in electronic circuits. Thispenalty P can then be integrated across the visible light spectrum:$\begin{matrix}{P = {\int_{\lambda_{\min}}^{\lambda_{\max}}\quad{{P\left( \lambda_{i} \right)}{\mathbb{d}\lambda}}}} & (7)\end{matrix}$

It is this metric that is optimized (reduced and/or minimized) by theprocess 600. Ultimately, this metric includes effects of significantinterferents as well as bleed-through from the excitation signal. Thesefactors that attenuate the signal in the excitation path, sample,emission path, and filtering properties of the excitation and emissionpaths can be adjusted by the user. The process 600 uses these parametersin combination with the targeted fluorophor and sample 108characteristics to generate a ranked series of LED configurations thatreduce the penalty metric P.

In a block 618, the process 600 compares the leakage penalties for eachpermutation of LEDs in the LED array 102. Results generated by theprocess 600 for evaluating GFPuv are shown in FIG. 7 for (a) anoptimized excitation spectrum, and (b) a non-optimized configuration.

In a block 620, the process 600 ranks the permutations of LEDs in theLED array 102 based on the comparison of their respective leakagepenalties.

In a block 622, for each permutation of the LEDs in the LED array 102the process 600 determines a duty cycle in the range of one percent totwelve percent for the drive current based on the leakage penalty.

In a block 624, for each permutation of the LEDs in the LED array 102the process 600 determines a drive current for each LED in the LED array102 based on the leakage penalty. In one embodiment, the drive currentis significantly in excess of a rated maximum current for the at leastone LED in the LED array 102. In a process 626, the process 600finishes.

In one embodiment, the process 600 has been optimized in arepresentative application for the excitation of GFPuv and has beencompared to a single LED light source. The simulation parameters arechosen for proof-of-concept only. Although most fluorescence systems usesome sort of optical filtering to reduce the interference of excitationwith emission signal, it is possible, within the flexibility andmodularity of the process 600 that some applications (that measurespectra rather than total intensity) will not require optical filteringand hence will not suffer from the optical losses associated with suchfiltering. Interfering effects such as autofluorescence and Ramanscattering can be implemented into the current the process 600 and maybe used to optimize even more accurately the system design to the needsof the targeted application.

Currently, the system 100 has a database consisting of several LEDS(blue, blue-green, green and purple) operating at drive currents from 1mA to 100 mA (corresponding to spectral shifts from 0 nm to 10 nm fromthe peak wavelength at nominal operation). The penalty metric describedin the previous section is minimized to determine the optimalcombination of LEDs for each application.

The process 600 rates a range of optimizing LED combinations bycomparing penalty calculations. The penalty for the best configurationis calculated at 0.159, compared to the less efficient non-optimizedconfiguration at 0.365. The emission spectra resulting from theexcitation by the closest matching single LED is compared to the GFPuvabsorption spectra in FIG. 7(c). From the data plotted in these figures,it can be shown that the optimized spectrum from the LED array 102reduces the excitation signal leakage into the output path and improvesthe emission signal that can be collected for interpretation.Performance improvements over single LED excitation show a 70.1%increase in collected emission signal for GFPuv fluorophors. The bestnon-optimized and single LED configurations are shown in Table 1 below.TABLE 1 Configurations for GFPuv fluorophors Configuration LEDs CurrentBest 1 purple 10 mA 2 purple 20 mA 2 purple 50 mA Non-optimized 1 blue10 mA 1 blue 100 mA  2 purple 20 mA 1 purple 10 mA Single LED 1 purple50 mA

FIG. 8 compares all three emission spectrum from FIG. 7 to demonstratethe analysis that is achieved by the process 600 in determining theoptimal configuration of LEDs in the LED array 102. A 70.4% improvementin the excitation signal over the single LED is achieved by the bestconfiguration. These improvements support the use of design optimizationof process 600 prior to the experimentation and fluorescent signalanalysis.

In an alternative embodiment, the optimal configuration provided by theprocess 600 may be implemented in a 5-element LED array 102 with the LEDdriver 120 to reduce the duty cycle to the LEDs (for improvingreliability and lifetime of the over driven LEDs). The outputs of theLEDs may then be coupled into a randomized fiber optic bundle to providea uniform input to the sample under analysis (eliminating the imagingartifacts common to many white light sources). In this experimentalembodiment, the LED array 102 and fiber optic bundle 104 may be coupledinto a Shimadzu RF3401 fluorometer and the outputs measured in a mannercomparable to when a Xenon source is used for sample 108 excitation. Inone embodiment, the LED configuration is optimized for threerepresentative applications as follows: (1) a theoretical desiredspectral output; (2) the excitation of Rhodamine dye; and (3) theexcitation of bacteria; GFPuv is cloned into Methylobacterium extorquensAM123, such that when suspended in liquid media, the fluorescentintensity of the cells is indicative of the cell concentration.

To demonstrate the capability of this LED array 102 over its closestalternatives, a desired spectrum is arbitrarily generated as shown inFIG. 9. Three possibilities for matching the LED spectrum to actual LEDoutput are shown: (a) the closest single LED; (b) the closestcombination of four types of LEDs operating under nominal conditions(with no spectral shift); and (c) the closest combination of four typesof LEDs operating under nominal and overdrive conditions as described inthe previous section. Qualitatively, this figure shows that the bestmatch between desired and actual spectrum is achieved by the moreflexible array (the one consisting of LEDs operating at nominal andoverdrive conditions). The best matches (as measured by the errorbetween desired and actual spectra) are configured as follows for eachtype of LED array as shown in Table 2.

The best, non-optimized, and single LED configurations are shown inTable 2 below. TABLE 2 Configurations for GFPuv fluorophorsConfiguration LEDs Current 5 LEDs at nominal 1 blue 10 mA operation 1blue 10 mA 1 blue 20 mA 1 blue-green 10 mA 1 blue-green 20 mA 5 LEDs inoverdrive 1 blue 10 mA 1 blue 20 mA 1 blue 20 mA 1 blue-green 20 mA 1blue-green 100 mA  Single LED 1 blue 50 mA

To complement these simulation results, the optimization process 600 andLED array 102 have been tested on two representative applications. Thefirst application demonstrates that the LED array 102 is capable ofproducing an emission signal within 25% of the performance of the Xenonsource for a biological analysis application (FIG. 11). The bacteriaMethylobacterium extorquens AM123 is analyzed under identicalexperimental conditions for both the Xenon source and a five element LEDarray 102 consisting of purple LEDs operating at 20 mA (nominaloperation) and purple LEDs operating at 50 mA (overdrive operation).While nominal operation does not enable the LEDs to approach the poweroutput of the Xenon lamp, overdrive operation brings the LED generatedemission output within 25% of that produced by the Xenon source.

To demonstrate the increased efficiency of the LED array 102 presentedhere, the emission signal for the (a) single LED array and (b) optimizedLED array is presented for the excitation of Rhodamine dye (FIG. 10).Despite the fact that the single LED array 102 (the closest match of asingle LED excitation peak to the Rhodamine dye absorptioncharacteristics) has a much greater intensity than the optimized LEDarray 102, the emission signal improves twofold over the non-optimized,single LED array 102. The optimized LED array 102 consists of two blueLEDs operating at 5 mA and three purple LEDs operating at 5 mA.

Embodiments of the present invention may be implemented using hardware,software, or a combination thereof. In implementations using software,the software may be stored on a machine-accessible medium. Amachine-accessible medium includes any mechanism that may be adapted tostore and/or transmit information in a form accessible by a machine(e.g., a computer, network device, personal digital assistant,manufacturing tool, any device with a set of one or more processors,etc.). For example, a machine-accessible medium includes recordable andnon-recordable media (e.g., read only memory (ROM), random access memory(RAM), magnetic disk storage media, optical storage media, flash memorydevices, etc.), as recess as electrical, optical, acoustic, or otherform of propagated signals (e.g., carrier waves, infrared signals,digital signals, etc.).

In the above description, numerous specific details, such as, forexample, particular processes, materials, devices, and so forth, arepresented to provide a thorough understanding of embodiments of theinvention. One skilled in the relevant art will recognize, however, thatthe embodiments of the present invention may be practiced without one ormore of the specific details, or with other methods, components, etc. Inother instances, structures or operations are not shown or described indetail to avoid obscuring the understanding of this description.

Reference throughout this specification to “one embodiment” or “anembodiment” means that a particular feature, structure, process, block,or characteristic described in connection with an embodiment is includedin at least one embodiment of the present invention. Thus, theappearance of the phrases “in one embodiment” or “in an embodiment” invarious places throughout this specification does not necessarily meanthat the phrases all refer to the same embodiment. The particularfeatures, structures, or characteristics may be combined in any suitablemanner in one or more embodiments.

The terms used in the following claims should not be construed to limitembodiments of the invention to the specific embodiments disclosed inthe specification and the claims. Rather, the scope of embodiments ofthe invention is to be determined entirely by the following claims,which are to be construed in accordance with established doctrines ofclaim interpretation.

1. An apparatus for performing fluorescence analysis, comprising: lightemitting diodes (LEDs) to emit excitation light having a first colorand/or wavelength; control electronics to apply drive currents to theLEDs to cause the LEDs to emit the excitation light, wherein at leastone of the drive currents is greater than a nominal drive current forthe at least one LED, wherein at least one drive current has a low dutycycle; optics to couple the excitation light from the LEDs to a holderfor a fluorophor, the fluorophor to emit light having a second colorand/or wavelength in response to the excitation light; a photodetector;and optical fiber to couple the light having the second color from thefluorophor to the photodetector.
 2. The apparatus of claim 1, wherein atleast one drive current has a duty cycle between greater than zeropercent and less than or equal to twelve percent.
 3. The apparatus ofclaim 1, wherein the control electronics are further to pulse at leastone drive current to at least one LED.
 4. The apparatus of claim 3,wherein the drive current is greater that a rated maximum current forthe at least one LED.
 5. The apparatus of claim 3, wherein the controlelectronics comprise at least one emitter follower circuit and/or atleast one source follower circuit.
 6. The apparatus of claim 1, whereinthe first color is selected from at least one of blue, green, purple,and blue-green.
 7. The apparatus of claim 1, wherein the optics tocouple the excitation light from the LEDs to the fluorophor comprise anindividual optical fiber bundle coupled to an individual LED.
 8. Theapparatus of claim 7, wherein the optical fiber bundles are bundledtogether to aggregate the excitation light from the LEDs into a singlelight beam having a substantially uniform intensity profile and/or asubstantially uniform wavelength distribution and coupled the singlelight beam to the fluorophor.
 9. The apparatus of claim 8, wherein theoptical fiber bundles are bundled together in a random manner.
 10. Theapparatus of claim 8, further comprising a beam splitter to split off asmall portion of the single light beam.
 11. The apparatus of claim 10,further comprising circuitry to measure the intensity of the smallportion of the single light beam as a function of the color and/orwavelength.
 12. The apparatus of claim 11, further comprising circuitryto adjust at least one individual drive current to at least one LED inresponse to the measured intensity of the small portion of the singlelight beam.
 13. The apparatus of claim 11, wherein the circuitrycomprises a spectrophotometer.
 14. The apparatus of claim 8, furthercomprising at least one individual PIN diode coupled to at least oneindividual LED to detect the excitation light emitted from the at leastone individual LED.
 15. The apparatus of claim 14, further comprisingcircuitry to adjust at least one individual drive current to the atleast one LED in response to the detected excitation light emitted fromthe at least one individual LED.
 16. The apparatus of claim 1, whereinthe holder for the fluorophor is a cuvette.
 17. The apparatus of claim1, wherein the photodetector is selected from at least one of aphotomultiplier tube, an avalanche photodiode, photodiode,phototransistor, and a charge-coupled device (CCD).
 18. An article ofmanufacture for selecting a configuration of an array of light emittingdiodes (LEDs) for placement in a fluorescence analysis system, the LEDarray to emit light to excite a fluorophor, the article of manufacturecomprising: a machine-accessible medium including data that, whenaccessed by a machine, cause the machine to perform the operationscomprising: determining at least two possible permutations of LEDs forthe LED array; for each permutation of LEDs in the LED array:determining a total excitation light that is to be emitted from the LEDarray; determining an amount of excitation light that is to reach thefluorophor based on the total excitation light emitted from the LEDarray; determining an amount of light that is to be transmitted throughthe fluorophor based on the amount of excitation light that is to reachthe fluorophor, based on an amount of attenuation in an emission path toa photodetector from the fluorophor in the fluorescence analysis system,and based on filtering of the light that is to be transmitted throughthe fluorophor; determining an amount of light that is to be emitted bythe fluorophor based on the amount of excitation light that is to reachthe fluorophor and based on the amount of light that is to betransmitted through the fluorophor; determining an amount of light thatis to reach the photodetector based on the amount of light that is to beemitted by the fluorophor; and determining a leakage penalty for thefluorescence analysis system based on the amount of light that is to betransmitted through the fluorophor and based on the amount of light thatis to reach the photodetector; comparing the leakage penalties for eachpermutation of LEDs in the LED array; and ranking the permutations ofLEDs in the LED array based on the comparison of their respectiveleakage penalties.
 19. The article of manufacture of claim 18, whereinthe machine-accessible medium further includes data that cause themachine to perform operations comprising receiving informationassociated with a type of LEDs to be selected from a database.
 20. Thearticle of manufacture of claim 19, wherein the machine-accessiblemedium further includes data that cause the machine to performoperations comprising receiving information associated with a number ofLEDs to be placed in the LED array.
 21. The article of manufacture ofclaim 20, wherein the machine-accessible medium further includes datathat cause the machine to perform operations comprising receivinginformation associated with the fluorophor of interest.
 22. The articleof manufacture of claim 21, wherein the machine-accessible mediumfurther includes data that cause the machine to perform operationscomprising receiving information associated with at least oneundesirable fluorophor.
 23. The article of manufacture of claim 22,wherein the machine-accessible medium further includes data that causethe machine to perform operations comprising receiving informationassociated with a minimum concentration detection capability for thefluorophor of interest.
 24. The article of manufacture of claim 23,wherein the machine-accessible medium further includes data that causethe machine to perform operations comprising receiving informationassociated with a time frame within which to perform fluorescenceanalysis on the fluorophor of interest.
 25. The article of manufactureof claim 18, wherein the machine-accessible medium further includes datathat cause the machine to perform operations comprising, for eachpermutation of LEDs in the LED array, determining optical power and/orspectral shape of an aggregate output of the LED array.
 26. The articleof manufacture of claim 18, wherein the machine-accessible mediumfurther includes data that cause the machine to perform operationscomprising, for each permutation of LEDs in the LED array, receivinginformation associated with spectral characteristics of thephotodetector.
 27. The article of manufacture of claim 26, wherein themachine-accessible medium further includes data that cause the machineto perform operations comprising, for each permutation of LEDs in theLED array, calculating output current and/or output voltage of thephotodetector based on the information associated with the spectralcharacteristics of the photodetector.
 28. The article of manufacture ofclaim 18, wherein the machine-accessible medium further includes datathat cause the machine to perform operations comprising, for eachpermutation of LEDs in the LED array, determining a drive current foreach LED in the LED array based on the leakage penalty.
 29. The articleof manufacture of claim 28, wherein the machine-accessible mediumfurther includes data that cause the machine to perform operationscomprising, for each permutation of LEDs in the LED array, determining aduty cycle for the drive current based on the leakage penalty.
 30. Thearticle of manufacture of claim 28, wherein the machine-accessiblemedium further includes data that cause the machine to performoperations comprising, for each permutation of LEDs in the LED array,determining a duty cycle in the range of one percent to twelve percentfor the drive current based on the leakage penalty.
 31. A method forselecting a configuration of an array of light emitting diodes (LEDs)for placement in a fluorescence analysis system, the LED array to emitlight to excite a fluorophor, the method: determining at least twopossible permutations of LEDs for the LED array; for each permutation ofLEDs in the LED array: determining a total excitation light that is tobe emitted from the LED array; determining an amount of excitation lightthat is to reach the fluorophor based on the total excitation lightemitted from the LED array; determining an amount of light that is to betransmitted through the fluorophor based on the amount of excitationlight that is to reach the fluorophor, based on an amount of attenuationin an emission path to a photodetector from the fluorophor in thefluorescence analysis system, and based on filtering of the light thatis to be transmitted through the fluorophor; determining an amount oflight that is to be emitted by the fluorophor based on the amount ofexcitation light that is to reach the fluorophor and based on the amountof light that is to be transmitted through the fluorophor; determiningan amount of light that is to reach the photodetector based on theamount of light that is to be emitted by the fluorophor; and determininga leakage penalty for the fluorescence analysis system based on theamount of light that is to be transmitted through the fluorophor andbased on the amount of light that is to reach the photodetector;comparing the leakage penalties for each permutation of LEDs in the LEDarray; and ranking the permutations of LEDs in the LED array based onthe comparison of their respective leakage penalties.
 32. The method ofclaim 31, further comprising, for each permutation of LEDs in the LEDarray, determining a duty cycle in the range of one percent to twelvepercent for the drive current based on the leakage penalty.
 33. Themethod of claim 32, further comprising, for each permutation of LEDs inthe LED array, determining a drive current for each LED in the LED arraybased on the leakage penalty, the drive current being significantly inexcess of a rated maximum current for the LED.